The main objective of this study is to examine the influence of the transport system on CO2 emission levels. To achieve this goal, first, identify existing interrelationships between transport performance indicators and CO2 emissions was established, and the direction and degree of impact of significant performance indicators of the transport system on emissions were assessed. Next, based on analysis and synthesis of the literature – both domestic and foreign – factors that have the greatest influence on the level of CO2 emissions were identified and systematized. Assuming that there are causal relationships between the amount of CO2 emissions and the performance of the transport system, three hypotheses were put forward. To test the hypotheses, two models – end-to-end regression and regressions with effects – were considered to characterize the dependence of CO2 emissions on transport system performance. Model testing was conducted to choose the best model for analysis. It was found that the fixed-effects regression model is preferable to the random-effects and end-to-end regression models with regard to identifying and assessing the transport system indicators that can be managed to improve environmental conditions in various regions of the Russian Federation.